Logging started at 15:32:44 on 09 Apr 2013
QIIME version: 1.6.0-dev

qiime_config values:
blastmat_dir	/Applications/blast-2.2.22/data/
sc_queue	all.q
topiaryexplorer_project_dir	/Users/caporaso/code/TopiaryExplorer-0.9.1/
pynast_template_alignment_fp	/Users/caporaso/data/greengenes_core_sets/core_set_aligned_imputed.fasta_11_8_07.no_dots
cluster_jobs_fp	start_parallel_jobs.py
assign_taxonomy_reference_seqs_fp	/Users/caporaso/data/gg_12_10_otus/rep_set/97_otus.fasta
torque_queue	friendlyq
template_alignment_lanemask_fp	/Users/caporaso/data/greengenes_core_sets/lanemask_in_1s_and_0s.txt
jobs_to_start	2
cloud_environment	False
qiime_scripts_dir	/Users/caporaso/code/Qiime/scripts
denoiser_min_per_core	50
python_exe_fp	python
temp_dir	/Users/caporaso/temp
blastall_fp	blastall
seconds_to_sleep	1
assign_taxonomy_id_to_taxonomy_fp	/Users/caporaso/data/gg_12_10_otus/taxonomy/97_otu_taxonomy.txt

parameter file values:
align_seqs:min_length	75
parallel:jobs_to_start	2
pick_otus:enable_rev_strand_match	True

Input file md5 sums:
/Users/caporaso/code/Qiime/qiime_test_data/pick_open_reference_otus/seqs1.fna: 094e424cf45cba69ef1c45fc7f61366f
/Users/caporaso/code/Qiime/qiime_test_data/pick_open_reference_otus/refseqs.fna: facf235fdcd71d1e99048705276103ab

Overridding similiary with 0.600.
Forcing --suppress_new_clusters as this is reference-based OTU picking.

Forcing --suppress_new_clusters as this is reference-based OTU picking.

Executing commands.

# Pick Reference OTUs (prefilter) command 
pick_otus.py -i /Users/caporaso/code/Qiime/qiime_test_data/pick_open_reference_otus/seqs1.fna -o /Users/caporaso/code/Qiime/qiime_test_data/pick_open_reference_otus/ucrss//prefilter_otus/ -r /Users/caporaso/code/Qiime/qiime_test_data/pick_open_reference_otus/refseqs.fna -m uclust_ref --similarity 0.6 --enable_rev_strand_match --suppress_new_clusters

Stdout:

Stderr:

# Filter prefilter failures from input command 
filter_fasta.py -f /Users/caporaso/code/Qiime/qiime_test_data/pick_open_reference_otus/seqs1.fna -o /Users/caporaso/code/Qiime/qiime_test_data/pick_open_reference_otus/ucrss//prefilter_otus//prefiltered_seqs1.fna -s /Users/caporaso/code/Qiime/qiime_test_data/pick_open_reference_otus/ucrss//prefilter_otus//seqs1_failures.txt -n

Stdout:

Stderr:

# Pick Reference OTUs command 
pick_otus.py -i /Users/caporaso/code/Qiime/qiime_test_data/pick_open_reference_otus/ucrss//prefilter_otus//prefiltered_seqs1.fna -o /Users/caporaso/code/Qiime/qiime_test_data/pick_open_reference_otus/ucrss//step1_otus -r /Users/caporaso/code/Qiime/qiime_test_data/pick_open_reference_otus/refseqs.fna -m uclust_ref --enable_rev_strand_match --suppress_new_clusters

Stdout:

Stderr:

# Generate full failures fasta file command 
filter_fasta.py -f /Users/caporaso/code/Qiime/qiime_test_data/pick_open_reference_otus/ucrss//prefilter_otus//prefiltered_seqs1.fna -s /Users/caporaso/code/Qiime/qiime_test_data/pick_open_reference_otus/ucrss//step1_otus/prefiltered_seqs1_failures.txt -o /Users/caporaso/code/Qiime/qiime_test_data/pick_open_reference_otus/ucrss//step1_otus/failures.fasta

Stdout:

Stderr:

Forcing --suppress_new_clusters as this is reference-based OTU picking.

Executing commands.

# Pick rep set command 
pick_rep_set.py -i /Users/caporaso/code/Qiime/qiime_test_data/pick_open_reference_otus/ucrss//step1_otus/prefiltered_seqs1_otus.txt -o /Users/caporaso/code/Qiime/qiime_test_data/pick_open_reference_otus/ucrss//step1_otus/step1_rep_set.fna -f /Users/caporaso/code/Qiime/qiime_test_data/pick_open_reference_otus/ucrss//prefilter_otus//prefiltered_seqs1.fna

Stdout:

Stderr:

# Pick de novo OTUs for new clusters command 
pick_otus.py -i /Users/caporaso/code/Qiime/qiime_test_data/pick_open_reference_otus/ucrss//step1_otus/subsampled_failures.fasta -o /Users/caporaso/code/Qiime/qiime_test_data/pick_open_reference_otus/ucrss//step2_otus/ -m uclust  --uclust_otu_id_prefix New.ReferenceOTU --enable_rev_strand_match

Stdout:

Stderr:

# Pick representative set for subsampled failures command 
pick_rep_set.py -i /Users/caporaso/code/Qiime/qiime_test_data/pick_open_reference_otus/ucrss//step2_otus//subsampled_failures_otus.txt -o /Users/caporaso/code/Qiime/qiime_test_data/pick_open_reference_otus/ucrss//step2_otus//step2_rep_set.fna -f /Users/caporaso/code/Qiime/qiime_test_data/pick_open_reference_otus/ucrss//step1_otus/subsampled_failures.fasta

Stdout:

Stderr:

# Pick reference OTUs using de novo rep set command 
pick_otus.py -i /Users/caporaso/code/Qiime/qiime_test_data/pick_open_reference_otus/ucrss//step1_otus/failures.fasta -o /Users/caporaso/code/Qiime/qiime_test_data/pick_open_reference_otus/ucrss//step3_otus/ -r /Users/caporaso/code/Qiime/qiime_test_data/pick_open_reference_otus/ucrss//step2_otus//step2_rep_set.fna -m uclust_ref --enable_rev_strand_match --suppress_new_clusters

Stdout:

Stderr:

# Create fasta file of step3 failures command 
filter_fasta.py -f /Users/caporaso/code/Qiime/qiime_test_data/pick_open_reference_otus/ucrss//step1_otus/failures.fasta -s /Users/caporaso/code/Qiime/qiime_test_data/pick_open_reference_otus/ucrss//step3_otus//failures_failures.txt -o /Users/caporaso/code/Qiime/qiime_test_data/pick_open_reference_otus/ucrss//step3_otus//failures_failures.fasta

Stdout:

Stderr:

# Pick de novo OTUs on step3 failures command 
pick_otus.py -i /Users/caporaso/code/Qiime/qiime_test_data/pick_open_reference_otus/ucrss//step3_otus//failures_failures.fasta -o /Users/caporaso/code/Qiime/qiime_test_data/pick_open_reference_otus/ucrss//step4_otus/ -m uclust  --uclust_otu_id_prefix New.CleanUp.ReferenceOTU --enable_rev_strand_match

Stdout:

Stderr:

# Merge OTU maps command 
cat /Users/caporaso/code/Qiime/qiime_test_data/pick_open_reference_otus/ucrss//step1_otus/prefiltered_seqs1_otus.txt /Users/caporaso/code/Qiime/qiime_test_data/pick_open_reference_otus/ucrss//step3_otus//failures_otus.txt /Users/caporaso/code/Qiime/qiime_test_data/pick_open_reference_otus/ucrss//step4_otus//failures_failures_otus.txt >> /Users/caporaso/code/Qiime/qiime_test_data/pick_open_reference_otus/ucrss//final_otu_map.txt

Stdout:

Stderr:

# Pick representative set for subsampled failures command 
pick_rep_set.py -i /Users/caporaso/code/Qiime/qiime_test_data/pick_open_reference_otus/ucrss//step4_otus//failures_failures_otus.txt -o /Users/caporaso/code/Qiime/qiime_test_data/pick_open_reference_otus/ucrss//step4_otus//step4_rep_set.fna -f /Users/caporaso/code/Qiime/qiime_test_data/pick_open_reference_otus/ucrss//step3_otus//failures_failures.fasta

Stdout:

Stderr:

Executing commands.

# Make the otu table command 
make_otu_table.py -i /Users/caporaso/code/Qiime/qiime_test_data/pick_open_reference_otus/ucrss//final_otu_map_mc2.txt -o /Users/caporaso/code/Qiime/qiime_test_data/pick_open_reference_otus/ucrss//otu_table_mc2.biom

Stdout:

Stderr:

Executing commands.

# Assign taxonomy command 
assign_taxonomy.py -o /Users/caporaso/code/Qiime/qiime_test_data/pick_open_reference_otus/ucrss//rdp_assigned_taxonomy -i /Users/caporaso/code/Qiime/qiime_test_data/pick_open_reference_otus/ucrss//rep_set.fna 

Stdout:

Stderr:

Executing commands.

# Add taxa to OTU table command 
add_metadata.py -i /Users/caporaso/code/Qiime/qiime_test_data/pick_open_reference_otus/ucrss//otu_table_mc2.biom --observation_mapping_fp /Users/caporaso/code/Qiime/qiime_test_data/pick_open_reference_otus/ucrss//rdp_assigned_taxonomy/rep_set_tax_assignments.txt -o /Users/caporaso/code/Qiime/qiime_test_data/pick_open_reference_otus/ucrss//otu_table_mc2_w_tax.biom --sc_separated taxonomy --observation_header OTUID,taxonomy

Stdout:

Stderr:

Executing commands.

# Align sequences command 
align_seqs.py -i /Users/caporaso/code/Qiime/qiime_test_data/pick_open_reference_otus/ucrss//rep_set.fna -o /Users/caporaso/code/Qiime/qiime_test_data/pick_open_reference_otus/ucrss//pynast_aligned_seqs --min_length 75

Stdout:

Stderr:

# Filter alignment command 
filter_alignment.py -o /Users/caporaso/code/Qiime/qiime_test_data/pick_open_reference_otus/ucrss//pynast_aligned_seqs -i /Users/caporaso/code/Qiime/qiime_test_data/pick_open_reference_otus/ucrss//pynast_aligned_seqs/rep_set_aligned.fasta 

Stdout:

Stderr:

# Build phylogenetic tree command 
make_phylogeny.py -i /Users/caporaso/code/Qiime/qiime_test_data/pick_open_reference_otus/ucrss//pynast_aligned_seqs/rep_set_aligned_pfiltered.fasta -o /Users/caporaso/code/Qiime/qiime_test_data/pick_open_reference_otus/ucrss//rep_set.tre 

Stdout:

Stderr:

Executing commands.


Logging stopped at 15:34:36 on 09 Apr 2013
